A novel technique based on photonic crystals (PC) will be developed and used to construct an extremely sensitive instrument for the study of biomolecular affinities and binding kinetics. We have previously demonstrated that a narrow midgap transmission peak can be formed and a local field enhancement can be achieved when a defect layer is sandwiched between two PCs. In this R21 application, we will explore for the first time the possibility to use only one PC in a total internal reflection geometry, so that the defect layer becomes accessible for binding of analyte molecules. When the defect layer is doped with absorbing materials, the spectrum of the reflected light from this PC structure will have a very narrow but prominent dip due to the enhanced absorption in the defect layer. The dip wavelength will depend very sensitively on the thickness and/or refractive index of the biomolecules bound to the defect layer. This will enable highly sensitive measurements of the binding of biomolecules and the kinetics of this process. We will focus on developing this novel methodology and constructing a highly sensitive PC based instrument. First, we will optimize our design of the PC structure based on comprehensive theoretical modeling and numerical simulations in order to achieve the maximum detection sensitivity. Then we will construct a working system using the optimized PC structure as a critical component. We will also explore several possible detection modes and develop related software for data analysis and interpretation. Finally, this instrument will be tested using several biological model systems in order to demonstrate its applicability. This new instrument will possess a number of advantages over the currently widely used surface plasmon resonance (SPR) based instrument and other waveguide based instruments. It will have the capability to study, in a quantitative manner and without requirement of labeling, many different dynamic molecular interactions in real time, allowing affinity measurements, concentration determinations of specific analytes, and kinetic analyses. We will compare directly the sensitivity of our technique to that of commercially available state-of- the-art SPR-based systems. CRITIQIUE